ArticleMicrobial genomics2023
SOCfinder: a genomic tool for identifying social genes in bacteria.
Article in Microbial genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
10 citing papers in PubMed, 10 citations in OpenAlex.
- Harnessing lytic phages for biofilm control in carbapenem-resistantMicrobiology spectrum · 2026Article
- A 'Genome-First' Framework for Next-Generation Bioinputs: From Functional Mining to Rational Synthetic Microbial Communities.Environmental microbiology · 2026Review
- The Evolutionary and Ecological Consequences of Cooperation.The American naturalist · 2026Review
- Cooperation and the evolution of bacterial niche breadth.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Studying adaptation at the invisible scale.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Article
- Host Transcriptomics Reveal Reduction in Defence-Reproduction Trade-Offs During Coinfection.Molecular ecology · 2025Article
- A phylogenetic approach to comparative genomics.Nature reviews. Genetics · 2025Review
- A reassessment of the infra-species diversity patterns in the wine-associatedFrontiers in microbiology · 2025Article
- Genes for cooperation are not more likely to be carried by plasmids.Proceedings. Biological sciences · 2024Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bacteria cooperate by working collaboratively to defend their colonies, share nutrients, and resist antibiotics. Nevertheless, our understanding of these remarkable behaviours primarily comes from studying a few well-characterized species. Consequently, there is a significant gap in our understanding of microbial social traits, particularly in natural environments. To address this gap, we can use bioinformatic tools to identify genes that control cooperative or otherwise social traits. Existing tools address this challenge through two approaches. One approach is to identify genes that encode extracellular proteins, which can provide benefits to neighbouring cells. An alternative approach is to predict gene function using annotation tools. However, these tools have several limitations. Not all extracellular proteins are cooperative, and not all cooperative behaviours are controlled by extracellular proteins. Furthermore, existing functional annotation methods frequently miss known cooperative genes. We introduce SOCfinder as a new tool to find bacterial genes that control cooperative or otherwise social traits. SOCfinder combines information from several methods, considering if a gene is likely to [1] code for an extracellular protein [2], have a cooperative functional annotation, or [3] be part of the biosynthesis of a cooperative secondary metabolite. We use data on two extensively-studied species (
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.